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Extracting the sequence of isoforms from RNA-seq data

Hello, I have a basic doubt. I have used rMATs to predict alternative splice events in my data. Then I am using IGV to built the sashimi plots to view the junction and exonic reads. Any idea how to extract the sequence for the isoforms ? The organism I am working on has the sequences given only for the primary transcript. How do I extract the novel isoform sequences ?

Thanks.

rna-seq
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updated by michael.ante michael.ante • written by pixie@bioinfo pixie@bioinfo

1 answer

Hi Pixie,

There are some tools available:

  • StringTie's / Cufflink's gffread
  • Bedtools getFastaFromBed
  • BedOps bed2faidx

Cheers,

Michael

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written by michael.ante michael.ante

Thanks Michael, I will check those out!

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written by pixie@bioinfo pixie@bioinfo

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